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  • 201.
    Huang, Yanyan
    et al.
    Mem Univ Newfoundland, Canada.
    Wille, Michelle
    Mem Univ Newfoundland, Canada.
    Dobbin, Ashley
    Mem Univ Newfoundland, Canada.
    Robertson, Gregory J
    Environm Canada, Wildlife Res Div, Canada.
    Ryan, Pierre
    Environm Canada, Canadian Wildlife, Canada.
    Ojkic, Davor
    Univ Guelph, Canada.
    Whitney, Hugh
    Newfoundland & Labrador Dept Nat Resources, Canada.
    Lang, Andrew S
    Mem Univ Newfoundland, Canada.
    A 4-year study of avian influenza virus prevalence and subtype diversity in ducks of Newfoundland, Canada.2013In: Canadian journal of microbiology (Print), ISSN 0008-4166, E-ISSN 1480-3275, Vol. 59, no 10, p. 701-708Article in journal (Refereed)
    Abstract [en]

    The island of Newfoundland, Canada, is at the eastern edge of North America and has migratory bird connections with the continental mainland as well as across the North Atlantic Ocean. Here, we report a 4-year avian influenza virus (AIV) epidemiological study in ducks in the St. John's region of Newfoundland. The overall prevalence of AIV detection in ducks during this study was 7.2%, with American Black Ducks contributing the vast majority of the collected samples and the AIV positives. The juvenile ducks showed a significantly higher AIV detection rate (10.6%) compared with adults (3.4%). Seasonally, AIV prevalence rates were higher in the autumn (8.4%), but positives were still detected in the winter (4.6%). Preliminary serology tests showed a high incidence of previous AIV infection (20/38, 52.6%). A total of 43 viruses were characterized for their HA-NA or HA subtypes, which revealed a large diversity of AIV subtypes and little recurrence of subtypes from year to year. Investigation of the movement patterns of ducks in this region showed that it is a largely non-migratory duck population, which may contribute to the observed pattern of high AIV subtype turnover. Phylogenetic analysis of 4 H1N1 and one H5N4 AIVs showed these viruses were highly similar to other low pathogenic AIV sequences from waterfowl in North America and assigned all gene segments into American-avian clades. Notably, the H1N1 viruses, which were identified in consecutive years, possessed homologous genomes. Such detection of homologous AIV genomes across years is rare, but indicates the role of the environmental reservoir in viral perpetuation.

  • 202.
    Huang, Yanyan
    et al.
    Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada.
    Wille, Michelle
    Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada.
    Dobbin, Ashley
    Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada.
    Walzthöni, Natasha M
    Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada.
    Robertson, Gregory J
    2 Wildlife Research Division, Environment Canada, Mount Pearl, Newfoundland and Labrador, Canada.
    Ojkic, Davor
    Animal Health Laboratory, University of Guelph, Guelph, Ontario, Canada.
    Whitney, Hugh
    Newfoundland and Labrador Department of Natural Resources, St. John’s, Newfoundland and Labrador, Canada.
    Lang, Andrew S
    Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada.
    Genetic structure of avian influenza viruses from ducks of the Atlantic flyway of North America.2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 1, p. Article ID: e86999-Article in journal (Refereed)
    Abstract [en]

    Wild birds, including waterfowl such as ducks, are reservoir hosts of influenza A viruses. Despite the increased number of avian influenza virus (AIV) genome sequences available, our understanding of AIV genetic structure and transmission through space and time in waterfowl in North America is still limited. In particular, AIVs in ducks of the Atlantic flyway of North America have not been thoroughly investigated. To begin to address this gap, we analyzed 109 AIV genome sequences from ducks in the Atlantic flyway to determine their genetic structure and to document the extent of gene flow in the context of sequences from other locations and other avian and mammalian host groups. The analyses included 25 AIVs from ducks from Newfoundland, Canada, from 2008-2011 and 84 available reference duck AIVs from the Atlantic flyway from 2006-2011. A vast diversity of viral genes and genomes was identified in the 109 viruses. The genetic structure differed amongst the 8 viral segments with predominant single lineages found for the PB2, PB1 and M segments, increased diversity found for the PA, NP and NS segments (2, 3 and 3 lineages, respectively), and the highest diversity found for the HA and NA segments (12 and 9 lineages, respectively). Identification of inter-hemispheric transmissions was rare with only 2% of the genes of Eurasian origin. Virus transmission between ducks and other bird groups was investigated, with 57.3% of the genes having highly similar (≥99% nucleotide identity) genes detected in birds other than ducks. Transmission between North American flyways has been frequent and 75.8% of the genes were highly similar to genes found in other North American flyways. However, the duck AIV genes did display spatial distribution bias, which was demonstrated by the different population sizes of specific viral genes in one or two neighbouring flyways compared to more distant flyways.

  • 203.
    Hubalek, Valerie
    et al.
    Uppsala University.
    Wu, Xiaofen
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Eiler, Alexander
    Uppsala University.
    Buck, Moritz
    Uppsala University.
    Heim, Christine
    Univ Göttingen, Germany.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bertilsson, Stefan
    Uppsala University.
    Ionescu, Danny
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Germany.
    Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 10, p. 2447-2458Article in journal (Refereed)
    Abstract [en]

    Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.

  • 204.
    Hugerth, Luisa W.
    et al.
    KTH Royal Institute of Technology.
    Larsson, John
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Alneberg, Johannes
    KTH Royal Institute of Technology.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Andersson, Anders F.
    KTH Royal Institute of Technology.
    Metagenome-assembled genomes uncover a global brackish microbiome2015In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 16, article id 279Article in journal (Refereed)
    Abstract [en]

    Background: Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. Results: We use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing thegenomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts. Conclusions: We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.

  • 205.
    Högfors-Rönnholm, Eva
    et al.
    Novia Univ Appl Sci, Finland.
    Christel, Stephan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dalhem, Krister
    Åbo Akad Univ, Finland.
    Lillhonga, Tom
    Novia Univ Appl Sci, Finland.
    Engblom, Sten
    Novia Univ Appl Sci, Finland.
    Österholm, Peter
    Åbo Akad Univ, Finland.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils2018In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 625, p. 39-49Article in journal (Refereed)
    Abstract [en]

    Naturally occurring sulfide rich deposits are common along the northern Baltic Sea coast thatwhen exposed to air, release large amounts of acid and metals into receiving water bodies. This causes severe environmental implications for agriculture, forestry, and building of infrastructure. In this study, we investigated the efficiency of ultrafine-grained calcium carbonate and peat (both separately and in combination) to mitigate acid and metal release. The experiments were carried out aerobically that mimicked summer conditions when the groundwater level is low and acid sulfate soils are exposed to oxygen, and anaerobically that is similar to autumn to spring conditions. The ultrafine-grained calcium carbonate dissipated well in the soil and its effect alone and when mixed with peat raised the pH and reduced pyrite dissolution while peat alone was similar to the controls and did not halt metal and acid release. High throughput 16S rRNA gene sequencing identified populations most similar to characterized acidophiles in the control and peat treated incubations while the acidophilic like populations were altered in the calcium carbonate alone and calcium carbonate plus peat treated acid sulfate soils. Coupled with the geochemistry data, it was suggested that the acidophiles were inactivated by the high pH in the presence of calcium carbonate but catalyzed pyrite dissolution in the controls and peat incubations. In conclusion, the anaerobic conditions during winter would likely be sufficient to mitigate acid production and metal release from acid sulfate soils and in the summer, treatment with calcium carbonate was the best mitigation method. (c) 2017 Elsevier B.V. All rights reserved.

  • 206.
    Högfors-Rönnholm, Eva
    et al.
    Novia Univ Appl Sci, Finland.
    Christel, Stephan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Engblom, Sten
    Novia Univ Appl Sci, Finland.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Indirect DNA extraction method suitable for acidic soil with high clay content2018In: MethodsX, ISSN 1258-780X, E-ISSN 2215-0161, Vol. 5, p. 136-140Article in journal (Refereed)
    Abstract [en]

    DNA extraction is an essential procedure when investigating microbial communities in environmental samples by sequencing technologies. High clay soils can be problematic as DNA adsorbs to the clay particles and can thereby be preserved from lysed, non-viable cells for a substantial period of time. In order to accurately estimate the intact and living microbial community in the soil, extracellular DNA from dead, remnant bacterial cells needs to be removed prior to DNA extraction. One possibility is to use a sodium phosphate buffer to release both extracellular DNA and bacterial cells from the clay particles. After removing the extracellular DNA by centrifugation, the remaining viable cells can be harvested and DNA extracted. The described method is a modification of a procedure for separating extracellular DNA and bacterial cells from acidic clay soils. The modified method increases bacterial cell yields from acidic clay soils, such as acid sulfate soil. The modified method eliminates some steps from the original method, as only DNA from intact bacterial cells is required. The indirect DNA extraction method increases the workload compared to standard direct extraction methods, but subsequent downstream analyses will give a more representative picture of the viable microbial community composition in the soil.

  • 207.
    Ianora, Adrianna
    et al.
    Stazione Zoologica Anton Dohrn, Italy.
    Bentley, Matthew G
    Newcastle University, UK.
    Caldwell, Gary S
    Newcastle University, UK.
    Casotti, Rafaella
    Stazione Zoologica Anton Dohrn, Italy.
    Cembella, Allan D
    Alfred Wegener Institute for Polar Research, Germany.
    Engström Öst, Jonna
    Novia University of Applied Sciences, Finland ; Åbo Akademi University, Finland.
    Halsband, Claudia
    Plymouth Marine Laboratory, UK.
    Sonnenschein, Eva
    International Max Planck Research School of Marine Microbiology, Germany.
    Legrand, Catherine
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Llewellyn, Carole
    Plymouth Marine Laboratory, UK.
    Paldaviciene, Aiste
    Klaipeda University, Lithuania.
    Pilkaityte, Renata
    Klaipeda University, Lithuania.
    Pohnert, Georg
    Friedrich Schiller University Jena, Germany.
    Razinkovas, Arthur
    Klaipeda University, Lithuania.
    Romano, Giovanna
    Stazione Zoologica Anton Dohrn, Italy.
    Tillmann, Urban
    Alfred Wegener Institute for Polar Research, Germany.
    Vaiciute, Diana
    Klaipeda University, Lithuania.
    The Relevance of Marine Chemical Ecology to Plankton and Ecosystem Function: An Emerging Field2011In: Marine Drugs, ISSN 1660-3397, E-ISSN 1660-3397, Vol. 9, no 9, p. 1625-1648Article in journal (Refereed)
    Abstract [en]

    Marine chemical ecology comprises the study of the production and interaction of bioactive molecules affecting organism behavior and function. Here we focus on bioactive compounds and interactions associated with phytoplankton, particularly bloom-forming diatoms, prymnesiophytes and dinoflagellates. Planktonic bioactive metabolites are structurally and functionally diverse and some may have multiple simultaneous functions including roles in chemical defense (antipredator, allelopathic and antibacterial compounds), and/or cell-to-cell signaling (e.g., polyunsaturated aldehydes (PUAs) of diatoms). Among inducible chemical defenses in response to grazing, there is high species-specific variability in the effects on grazers, ranging from severe physical incapacitation and/or death to no apparent physiological response, depending on predator susceptibility and detoxification capability. Most bioactive compounds are present in very low concentrations, in both the producing organism and the surrounding aqueous medium. Furthermore, bioactivity may be subject to synergistic interactions with other natural and anthropogenic environmental toxicants. Most, if not all phycotoxins are classic secondary metabolites, but many other bioactive metabolites are simple molecules derived from primary metabolism (e.g., PUAs in diatoms, dimethylsulfoniopropionate (DMSP) in prymnesiophytes). Producing cells do not seem to suffer physiological impact due to their synthesis. Functional genome sequence data and gene expression analysis will provide insights into regulatory and metabolic pathways in producer organisms, as well as identification of mechanisms of action in target organisms. Understanding chemical ecological responses to environmental triggers and chemically-mediated species interactions will help define crucial chemical and molecular processes that help maintain biodiversity and ecosystem functionality.

  • 208.
    Ininbergs, Karolina
    et al.
    Stockholm University.
    Bergman, Birgitta
    Stockholm University.
    Larsson, John
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University.
    Ekman, Martin
    Stockholm University.
    Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring2015In: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 44, p. S439-S450Article in journal (Refereed)
    Abstract [en]

    Metagenomics refers to the analysis of DNA from a whole community. Metagenomic sequencing of environmental DNA has greatly improved our knowledge of the identity and function of microorganisms in aquatic, terrestrial, and human biomes. Although open oceans have been the primary focus of studies on aquatic microbes, coastal and brackish ecosystems are now being surveyed. Here, we review so far published studies on microbes in the Baltic Sea, one of the world's largest brackish water bodies, using high throughput sequencing of environmental DNA and RNA. Collectively the data illustrate that Baltic Sea microbes are unique and highly diverse, and well adapted to this brackish-water ecosystem, findings that represent a novel base-line knowledge necessary for monitoring purposes and a sustainable management. More specifically, the data relate to environmental drivers for microbial community composition and function, assessments of the microbial biodiversity, adaptations and role of microbes in the nitrogen cycle, and microbial genome assembly from metagenomic sequences. With these discoveries as background, prospects of using metagenomics for Baltic Sea environmental monitoring are discussed.

  • 209.
    Isaksson, Jenny
    et al.
    Uppsala University.
    Christerson, Linus
    Uppsala University.
    Blomqvist, Maria
    Uppsala University.
    Wille, Michelle
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Alladio, Lucia A.
    Univ Nacl Andres Bello, Chile.
    Sachse, Konrad
    Friedrich Loeffler Inst, Germany.
    Olsen, Björn
    Uppsala University.
    Gonzalez-Acuna, Daniel
    Univ Concepcion, Chile.
    Herrmann, Bjorn
    Uppsala University.
    Chlamydiaceae-like bacterium, but no Chlamydia psittaci, in sea birds from Antarctica2015In: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056, Vol. 38, no 11, p. 1931-1936Article in journal (Refereed)
    Abstract [en]

    Within the growing order of Chlamydiales, there are a number of pathogens. One is Chlamydia psittaci, a zoonotic pathogen, with birds as natural hosts that may be transmitted to humans and cause severe respiratory disease, psittacosis. The prevalence of this pathogen in Antarctic birds is almost unknown as well as the ramifications of its potential spread in na < ve bird populations. To investigate the prevalence of chlamydia organisms, cloacal and fecal samples were collected from 264 penguins and 263 seabirds on the Antarctic Peninsula and in Southern Chile. No C. psittaci could be detected by 23S rRNA real-time PCR. However, DNA sequencing of the 16S rRNA 298-bp signature sequence revealed a Chlamydiaceae-like bacterium previously found in seabirds from the subarctic zone, demonstrating that this not yet fully characterized bacterium is widespread. In conclusion, the prevalence of C. psittaci among wild birds on the Antarctic Peninsula seems to be low, but other types of chlamydial organisms are common. Further studies are required to taxonomically define and finally understand the role of these non-classified Chlamydiae.

  • 210.
    Israelsson, Stina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bunse, Carina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Otago, New Zealand.
    Bertos-Fortis, Mireia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fridolfsson, Emil
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindehoff, Elin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University.
    Martinez-Garcia, Sandra
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Universidade de Vigo, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Seasonal dynamics of Baltic Sea plankton activities: heterotrophic bacterial function under different biological and environmental conditionsManuscript (preprint) (Other academic)
  • 211.
    Israelsson, Stina
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Jonsson, Nina
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Gullberg, Maria
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Technical University of Denmark, Denmark.
    Lindberg, A. Michael
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Cytolytic replication of echoviruses in colon cancer cell lines2011In: Virology Journal, ISSN 1743-422X, E-ISSN 1743-422X, Vol. 8, article id e473Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Colorectal cancer is one of the most common cancers in the world, killing nearly 50% of patients afflicted. Though progress is being made within surgery and other complementary treatments, there is still need for new and more effective treatments. Oncolytic virotherapy, meaning that a cancer is cured by viral infection, is a promising field for finding new and improved treatments. We have investigated the oncolytic potential of several low-pathogenic echoviruses with rare clinical occurrence. Echoviruses are members of the enterovirus genus within the family Picornaviridae.

    METHODS: Six colon cancer cell lines (CaCo-2, HT29, LoVo, SW480, SW620 and T84) were infected by the human enterovirus B species echovirus 12, 15, 17, 26 and 29, and cytopathic effects as well as viral replication efficacy were investigated. Infectivity was also tested in spheroids grown from HT29 cells.

    RESULTS: Echovirus 12, 17, 26 and 29 replicated efficiently in almost all cell lines and were considered highly cytolytic. The infectivity of these four viruses was further evaluated in artificial tumors (spheroids), where it was found that echovirus 12, 17 and 26 easily infected the spheroids.

    CONCLUSIONS: We have found that echovirus 12, 17 and 26 have potential as oncolytic agents against colon cancer, by comparing the cytolytic capacity of five low-pathogenic echoviruses in six colon cancer cell lines and in artificial tumors.

  • 212. Janson, Sven
    et al.
    Wouters, Johanna
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Bergman, Birgitta
    Carpenter, E. J.
    Host specificity in the Richelia-diatom symbiosis revealed by hetR gene sequence analysis1999In: Environmental Microbiology, ISSN 1462-2912, Vol. 1, no 5, p. 431-438Article in journal (Refereed)
  • 213.
    Jansson, Désirée S.
    et al.
    National Veterinary Institute.
    Mushtaq, Memoona
    Swedish University of Agricultural Sciences.
    Johansson, Karl-Erik
    Swedish University of Agricultural Sciences.
    Bonnedahl, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Kalmar County Hospital.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Andersson, Dan I.
    Uppsala University.
    Broman, Tina
    FOI – Swedish Defence Research Agency.
    Berg, Charlotte
    Swedish University of Agricultural Sciences.
    Olsen, Björn
    Uppsala University.
    Intestinal spirochaetes (genus Brachyspira) colonise wild birds in the southern Atlantic region and Antarctica2015In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 5, article id 29296Article in journal (Refereed)
    Abstract [en]

    INTRODUCTION: The genus Brachyspira contains well-known enteric pathogens of veterinary significance, suggested agents of colonic disease in humans, and one potentially zoonotic agent. There are recent studies showing that Brachyspira are more widespread in the wildlife community than previously thought. There are no records of this genus in wildlife from the southern Atlantic region and Antarctica. Our aim was therefore, to determine whether intestinal spirochaetes of genus Brachyspira colonise marine and coastal birds in this region.

    METHOD: Faecal samples were collected from marine and coastal birds in the southern Atlantic region, including sub-Antarctic islands and Antarctica, in 2002, 2009, and 2012, with the aim to isolate and characterise zoonotic agents. In total, 205 samples from 11 bird species were selectively cultured for intestinal spirochaetes of genus Brachyspira. To identify isolates to species level, they were subjected to phenotyping, species-specific polymerase chain reactions, sequencing of partial 16S rRNA, NADH oxidase (nox), and tlyA genes, and phylogenetic analysis. Antimicrobial susceptibility tests were performed.

    RESULTS: Fourteen unique strains were obtained from 10 birds of three species: four snowy sheathbills (Chionis albus), three kelp geese (Chloephaga hybrida subsp. malvinarum), and three brown skua (Stercorarius antarcticus subsp. lonnbergi) sampled on the Falkland Islands, Tierra del Fuego in Argentina, South Georgia, South Shetland Islands, and the Antarctic Peninsula. Five Brachyspira strains were closely related to potentially enteropathogenic Brachyspira sp. of chickens: B. intermedia (n=2, from snowy sheathbills), and B. alvinipulli (n=3, from a kelp goose and two snowy sheathbills). Three strains from kelp geese were most similar to the presumed non-pathogenic species 'B. pulli' and B. murdochii, whereas the remaining six strains could not be attributed to currently known species. No isolates related to human strains were found. None of the tested strains showed decreased susceptibility to tiamulin, valnemulin, doxycycline, tylvalosin, lincomycin, or tylosin.

    CONCLUSIONS: This is the first report of intestinal spirochaetes from this region. Despite limitations of current diagnostic methods, our results, together with earlier studies, show that Brachyspira spp., including potentially pathogenic strains, occur globally among free-living avian hosts, and that this genus encompasses a higher degree of biodiversity than previously recognised.

  • 214.
    Johansson, Olle
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Detektion av Fusobacterium necrophorum med realtids-PCR2010Independent thesis Basic level (university diploma), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Fusobacterium necrophorum are Gram-stain negative, anaerobic, bacteria that are grouped into subspecies necrophorum and funduliforme. Fusobacterium necrophorum ss. funduliforme has recently been suspected to play a role in common throat infections such as tonsillitis. The purpose of this work was to set up and test a method for real-time PCR (Polymerase Chain Reaction) according to Taqman with the purpose of detecting ss. funduliforme. We also examined how the storage time within transport medium (Amies charcoal, Copan) and culture medium (FAB-broth) affects the survival of the bacterium and the sensitivity of the culture and PCR methods. Bacterial suspensions of different concentrations were applied to pharyngeal sampling swabs and then directly incubated in transport medium. For each day the experiment lasted, a set of swabs of each concentration were cultured, DNA extracted, and real-time PCR performed. DNA extracted from ss. funduliforme was used as standards for the real-time PCR, with a minimum concentration of 10 DNA molecules per μL.

    Subspecies funduliforme could be detected from all days with real-time PCR while the cultures showed the best results if the sample was cultured within one day of collection. Real-time PCR can detect the presence of ss. funduliforme after prolonged storage and can therefore show accurate results for transported samples. Traditional culturing on growth medium is still a valuable and reliable method, provided that the samples are cultured within 24 hours. Culture may also be needed i.e. since PCR gives no information of the antibiotic resistance of the isolate.

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  • 215.
    Johansson, S
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Molecular characterization of Ljungan virus2001Conference paper (Refereed)
  • 216.
    Johansson, S
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Kinnunen, L
    University of Helsinki, Finland.
    Hyypiä, T
    University of Helsinki, Finland.
    Niklasson, B
    Uppsala University, Sweden.
    Ljungan virus: Genome analysis, genetic diversity and phylogenetic relationship to members of Picornaviridae1998Conference paper (Refereed)
  • 217.
    Johansson, S
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Niklasson, B
    Svensson, B
    Elfström, T
    Tesh, RB
    University of Texas, Galveston, USA.
    Lindberg, Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Molecular characterization of Ljungan virus strains - "new" members of the Picornaviridae2000In: EUROPIC 2000: XIth Meeting, Baia delle Zagare, Italy, 2000Conference paper (Refereed)
  • 218.
    Johansson, Susanne
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Niklasson, Bo
    Tesh, Robert
    Shafren, Darren
    Lindberg, Michael
    Molecular characterisation of M1146, an American isolate of Ljungan virus (LV) reveals the presence of a new LV genotypeManuscript (Other (popular science, discussion, etc.))
  • 219.
    Johansson, Susanne
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Polacek, Charlotta
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nilsson, Anne
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Ohlson, Sten
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, A. Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Studies of weak-to-moderate virus-receptor interactions using uncloned viruses as well as an infectious cDNA clone of echovirus 7 strain Wallace1996Conference paper (Refereed)
  • 220.
    Johri, Atul K.
    et al.
    Jawaharlal Nehru Univ, India.
    Oelmueller, Ralf
    Univ Jena, Germany.
    Dua, Meenakshi
    Jawaharlal Nehru Univ, India.
    Yadav, Vikas
    Jawaharlal Nehru Univ, India.
    Kumar, Manoj
    Jawaharlal Nehru Univ, India.
    Tuteja, Narendra
    Int Ctr Genet Engn & Biotechnol, India;Amity Univ, India.
    Varma, Ajit
    Amity Univ, India.
    Bonfante, Paola
    Univ Turin, Italy.
    Persson, Bengt L.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Stroud, Robert M.
    Univ Calif San Francisco, USA.
    Fungal association and utilization of phosphate by plants: success, limitations, and future prospects2015In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, article id 984Article, review/survey (Refereed)
    Abstract [en]

    Phosphorus (P) is a major macronutrient for plant health and development. The available form of P is generally low in the rhizosphere even in fertile soils. A major proportion of applied phosphate (Pi) fertilizers in the soil become fixed into insoluble, unavailable forms, which restricts crop production throughout the world. Roots possess two distinct modes of P uptake from the soil, direct and indirect uptake. The direct uptake of P is facilitated by the plant's own Pi transporters while indirect uptake occurs via mycorrhizal symbiosis, where the host plant obtains P primarily from the fungal partner, while the fungus benefits from plant-derived reduced carbon. So far, only one Pi transporter has been characterized from the mycorrhizal fungus Glomus versiforme. As arbuscular mycorrhizal fungi cannot be cultured axenically, their Pi transporter network is difficult to exploite for large scale sustainable agriculture. Alternatively, the root-colonizing endophytic fungus Piriformospora indica can grow axenically and provides strong growth-promoting activity during its symbiosis with a broad spectrum of plants. P indica contains a high affinity Pi transporter (PiPT) involved in improving Pi nutrition levels in the host plant under P limiting conditions. As P indica can be manipulated genetically, it opens new vistas to be used in P deficient fields.

  • 221.
    Jonsson, Nina
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Gullberg, Maria
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Israelsson, Stina
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, A. Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    A rapid and efficient method for studies of virus interaction at the host cell surface using enteroviruses and real-time PCR2009In: Virology Journal, ISSN 1743-422X, E-ISSN 1743-422X, Vol. 6, no Article ID: 217Article in journal (Refereed)
    Abstract [en]

    Background: Measuring virus attachment to host cells is of great importance when trying to identify novel receptors. The presence of a usable receptor is a major determinant of viral host range and cell tropism. Furthermore, identification of appropriate receptors is central for the understanding of viral pathogenesis and gives possibilities to develop antiviral drugs. Attachment is presently measured using radiolabeled and subsequently gradient purified viruses. Traditional methods are expensive and time-consuming and not all viruses are stable during a purification procedure; hence there is room for improvement. Real-time PCR (RT-PCR) has become the standard method to detect and quantify virus infections, including enteroviruses, in clinical samples. For instance, primers directed to the highly conserved 5' untranslated region (5'UTR) of the enterovirus genome enable detection of a wide spectrum of enteroviruses. Here, we evaluate the capacity of the RT-PCR technology to study enterovirus host cell interactions at the cell surface and compare this novel implementation with an established assay using radiolabeled viruses. Results: Both purified and crude viral extracts of CVB5 generated comparable results in attachment studies when analyzed with RT-PCR. In addition, receptor binding studies regarding viruses with coxsackie- nd adenovirus receptor (CAR) and/or decay accelerating factor (DAF) affinity, further demonstrated the possibility to use RT-PCR to measure virus attachment to host cells. Furthermore, the RT-PCR technology and crude viral extracts was used to study attachment with low multiplicity of infection (0.05 x 10(-4)TCID(50)/cell) and low cell numbers (250), which implies the range of potential implementations of the presented technique. Conclusion: We have implemented the well-established RT-PCR technique to measure viral attachment to host cells with high accuracy and reproducibility, at low cost and with less effort than traditional methods. Furthermore, replacing traditional methods with RT-PCR offers the opportunity to use crude virus containing extracts to investigate attachment, which could be considered as a step towards viral attachment studies in a more natural state.

  • 222.
    Jonsson, Nina
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Gullberg, Maria
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, A. Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Real-time polymerase chain reaction as a rapid and efficient alternative to estimation of picornavirus titers by tissue culture infectious dose 50% or plaque forming units2009In: Microbiology and immunology, ISSN 0385-5600, E-ISSN 1348-0421, Vol. 53, no 3, p. 149-154Article in journal (Refereed)
    Abstract [en]

    Quantification of viral infectious units is traditionally measured by methods based on forming plaques in semisolid media (PFU) or endpoint dilution of a virus-containing solution (TCID(50)), methods that are laborious, time-consuming and take on average 3-7 days to carry out. Quantitative real-time PCR is an established method to quantify nucleic acids at high accuracy and reproducibility, routinely used for virus detection and identification. In the present study, a procedure was developed using a two-step real-time PCR and the SYBR Green detection method to study whether there are correlations between TCID(50)/ml, PFU/ml and Ct values generated by real-time PCR enabling rapid and efficient calculation of titer equivalents when working with viruses in the research laboratory. In addition, an external standard with known concentrations was included using in vitro transcribed viral RNA, thus allowing the calculation of the amount of RNA copies needed for various applications (i.e. per plaque or TCID(50)).The results show that there is a correlation between the three quantification methods covering a wide range of concentration of viruses. Furthermore, a general regression line between TCID(50) and Ct values was obtained for all viruses included in the study, which enabled recording titer equivalents using real-time PCR. Finally, by including an external standard, the amount of RNA genomes generating one TCID(50) or PFU for each enterovirus serotype included was determined.

  • 223.
    Jonsson, Nina
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Wahlström, Kristin
    Svensson, Lennart
    Serrander, Lena
    Lindberg, A. Michael
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Aichi virus infection in elderly people in Sweden.2012In: Archives of Virology, ISSN 0304-8608, E-ISSN 1432-8798, Vol. 157, no 7, p. 1365-1369Article in journal (Refereed)
    Abstract [en]

    Aichi virus (AiV), genus Kobuvirus, family Picornaviridae, is associated with gastroenteritis in humans. Previous studies have shown high seroprevalence but low incidence (0.9-4.1%) in clinical samples. We report here the first detection of AiV in Sweden. Two hundred twenty-one specimens from hospitalized patients with diarrhea, who were negative for other enteric viruses, were included in the study. AiV were detected in three specimens, all from elderly patients. Phylogenetic analysis revealed that the three Swedish isolates belonged to genotype A and were genetically closest to European and Asian strains of AiV.

  • 224.
    Jourdain, Elsa
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Olsen, Björn
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Lundkvist, Ake
    Hubálek, Zdenek
    Sikutová, Silvie
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Karlsson, Malin
    Wahlström, Maria
    Jozan, Martine
    Falk, Kerstin I
    Surveillance for West Nile virus in wild birds from northern Europe.2011In: Vector Borne and Zoonotic Diseases, ISSN 1530-3667, E-ISSN 1557-7759, Vol. 11, no 1, p. 77-79Article in journal (Refereed)
    Abstract [en]

    A total of 1935 migratory birds from 104 different species were captured in southeastern Sweden in 2005-2006 and tested for antibodies against West Nile virus (WNV). Overall, 46 birds (2.4%; binomial confidence limits, 1.8-3.2) were positive by blocking-ELISA, but only 2 (0.10%; binomial confidence limits, 0.0-0.4) had antibodies detectable by both blocking-ELISA and WNV neutralization test. ELISA-positive birds included long- and short-distance migrants likely exposed to WNV while wintering in or migrating through areas enzootic for WNV. Exposure to a cross-reactive Flavivirus was suspected for short-distance migrants of the Turdidae family, but no cross-neutralization with tick-borne encephalitis and Usutu viruses was observed.

  • 225.
    Jourdain, Elsa
    et al.
    INRA, France.
    van Riel, Debby
    Erasmus Medical Center, The Netherlands.
    Munster, Vincent J
    National Institutes of Health, USA.
    Kuiken, Thijs
    Erasmus Medical Center, The Netherlands.
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Olsen, Björn
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Uppsala University.
    Ellström, Patrik
    Uppsala University.
    The pattern of influenza virus attachment varies among wild bird species2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 9, article id e24155Article in journal (Refereed)
    Abstract [en]

    The ability to attach to host cells is one of the main determinants of the host range of influenza A viruses. By using virus histochemistry, we investigate the pattern of virus attachment of both a human and an avian influenza virus in colon and trachea sections from 12 wild bird species. We show that significant variations exist, even between closely related avian species, which suggests that the ability of wild birds to serve as hosts for influenza viruses strongly varies among species. These results will prove valuable to assess the possibilities of interspecies transmission of influenza viruses in natural environments and better understand the ecology of influenza.

  • 226.
    Järhult, Josef D.
    et al.
    Uppsala University.
    Muradrasoli, Shaman
    Swedish University of Agricultural Sciences.
    Wahlgren, John
    Swedish Institute for Infectious Disease Control ; Karolinska Institutet.
    Söderström, Hanna
    Umeå University.
    Orozovic, Goran
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Gunnarsson, Gunnar
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Kristianstad University.
    Bröjer, Caroline
    National Veterinary Institute ; Swedish University of Agricultural Sciences.
    Latorre-Margalef, Neus
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Fick, Jerker
    Umeå University.
    Grabic, Roman
    Umeå University ; University of South Bohemia in Ceske Budejovice, Czech Republic.
    Lennerstrand, Johan
    Uppsala University.
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Lundkvist, Ake
    Swedish Institute for Infectious Disease Control ; Karolinska Institutet.
    Olsen, Björn
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Uppsala University.
    Environmental levels of the antiviral oseltamivir induce development of resistance mutation H274Y in influenza A/H1N1 virus in mallards2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 9, article id e24742Article in journal (Refereed)
    Abstract [en]

    Oseltamivir (Tamiflu®) is the most widely used drug against influenza infections and is extensively stockpiled worldwide as part of pandemic preparedness plans. However, resistance is a growing problem and in 2008-2009, seasonal human influenza A/H1N1 virus strains in most parts of the world carried the mutation H274Y in the neuraminidase gene which causes resistance to the drug. The active metabolite of oseltamivir, oseltamivir carboxylate (OC), is poorly degraded in sewage treatment plants and surface water and has been detected in aquatic environments where the natural influenza reservoir, dabbling ducks, can be exposed to the substance. To assess if resistance can develop under these circumstances, we infected mallards with influenza A/H1N1 virus and exposed the birds to 80 ng/L, 1 µg/L and 80 µg/L of OC through their sole water source. By sequencing the neuraminidase gene from fecal samples, we found that H274Y occurred at 1 µg/L of OC and rapidly dominated the viral population at 80 µg/L. IC₅₀ for OC was increased from 2-4 nM in wild-type viruses to 400-700 nM in H274Y mutants as measured by a neuraminidase inhibition assay. This is consistent with the decrease in sensitivity to OC that has been noted among human clinical isolates carrying H274Y. Environmental OC levels have been measured to 58-293 ng/L during seasonal outbreaks and are expected to reach µg/L-levels during pandemics. Thus, resistance could be induced in influenza viruses circulating among wild ducks. As influenza viruses can cross species barriers, oseltamivir resistance could spread to human-adapted strains with pandemic potential disabling oseltamivir, a cornerstone in pandemic preparedness planning. We propose surveillance in wild birds as a measure to understand the resistance situation in nature and to monitor it over time. Strategies to lower environmental levels of OC include improved sewage treatment and, more importantly, a prudent use of antivirals.

  • 227. Jääskeläinen, Anne J
    et al.
    Kolehmainen, Pekka
    Voutilainen, Liina
    Hauffe, Heidi C
    Kallio-Kokko, Hannimari
    Lappalainen, Maija
    Tolf, Conny
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindberg, A. Michael
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Henttonen, Heikki
    Vaheri, Antti
    Tauriainen, Sisko
    Vapalahti, Olli
    Evidence of ljungan virus specific antibodies in humans and rodents, Finland.2013In: Journal of Medical Virology, ISSN 0146-6615, E-ISSN 1096-9071, Vol. 85, no 11, p. 2001-2008Article in journal (Refereed)
    Abstract [en]

    Ljungan virus (LV, genus Parechovirus, family Picornaviridae) is considered currently to be a rodent-borne virus. Despite suggested human disease associations, its zoonotic potential remains unclear. To date, LV antibody prevalence in both humans and rodents has not been studied. In this study, two different LV immunofluorescence assays (LV IFAs) were developed with LV genotypes 1 (LV strain 87-012G) and 2 (LV strain 145SLG), and cross-neutralization and -reaction studies were carried out with LV strain 145SLG. Finally, a panel of 37 Finnish sera was screened for anti-LV antibodies using two different LV IFAs (LV 145SLG and LV 87-012G) and a neutralization (NT) assay (LV 145SLG), and 50 samples from Myodes glareolus by LV IFA (LV 145SLG). The LV seroprevalence study showed 38% and 18% positivity in humans and M. glareolus, respectively. LV IFAs and NT assays were compared, and the results were in good agreement. The data are the first evidence of humans and rodents coming into contact with LV in Finland. Additional studies are required in order to acquire a better understanding of the prevalence, epidemiological patterns and possible disease association of LV infections.

  • 228.
    Kaksonen, Anna H.
    et al.
    Tampere University of Technology, Tampere, Finland.
    Dopson, Mark
    Umeå University.
    Karnachuk, Olia V.
    Tomsk State University, Tomsk, Russia.
    Tuovinen, Olli H.
    Ohio State University, USA.
    Puhakka, Jaakko A.
    Tampere University of Technology, Tampere, Finland.
    Biological iron oxidation and sulfate reduction in the treatment of acid mine drainage at low temperatures2008In: Psychrophiles: From Biodiversity to Biotechnology, Book part 4 / [ed] Rosa Margesin, Franz Schinner, Jean-Claude Marx, Charles Gerday, Berlin: Springer, 2008, p. 429-454Chapter in book (Refereed)
    Abstract [en]

    Acid mine drainage (AMD) is the result of exposure of sulfidic seams to the oxidizing and leaching action of water—rain water, humidity, and groundwater— and is exacerbated by microorganisms that catalyze the solubilization of sulfide minerals by the regeneration of Fe3+ and oxidation of their dissolution products as the source of energy. Typical AMD has a low pH and a high sulfate and ferric iron concentration although other metals may also be present. The chemical composition of AMD varies with sulfide minerals associated with coal and metal mines. At low pH, ferric iron in AMD participates in the leaching action, as shown for pyrite (FeS2) and chalcopyrite (CuFeS2).

  • 229.
    Karlsson, Christofer M. G.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Cerro-Galvez, Elena
    CSIC, Spain.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Karlsson, Camilla
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Vila-Costa, Maria
    CSIC, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL3412019In: Microbial Biotechnology, ISSN 1751-7907, E-ISSN 1751-7915, Vol. 12, no 5, p. 892-906Article in journal (Refereed)
    Abstract [en]

    Organic pollutants (OPs) are critically toxic, bioaccumulative and globally widespread. Moreover, several OPs negatively influence aquatic wildlife. Although bacteria are major drivers of the ocean carbon cycle and the turnover of vital elements, there is limited knowledge of OP effects on heterotrophic bacterioplankton. We therefore investigated growth and gene expression responses of the Baltic Sea model bacterium Rheinheimera sp. BAL341 to environmentally relevant concentrations of distinct classes of OPs in 2-h incubation experiments. During exponential growth, exposure to a mix of polycyclic aromatic hydrocarbons, alkanes and organophosphate esters (denoted MIX) resulted in a significant decrease (between 9% and 18%) in bacterial abundance and production compared with controls. In contrast, combined exposure to perfluorooctanesulfonic acids and perfluorooctanoic acids (denoted PFAS) had no significant effect on growth. Nevertheless, MIX and PFAS exposures both induced significant shifts in gene expression profiles compared with controls in exponential growth. This involved several functional metabolism categories (e.g. stress response and fatty acids metabolism), some of which were pollutant-specific (e.g. phosphate acquisition and alkane-1 monooxygenase genes). In stationary phase, only two genes in the MIX treatment were significantly differentially expressed. The substantial direct influence of OPs on metabolism during bacterial growth suggests that widespread OPs could severely alter biogeochemical processes governed by bacterioplankton.

  • 230.
    Karlsson, Christofer M. G.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Karlsson, Camilla
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Teikari, Jonna E.
    University of Helsinki, Finland.
    Moran, Mary Ann
    University of Georgia, Athens, USA.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Different gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matterManuscript (preprint) (Other academic)
    Abstract [en]

    Phytoplankton release massive amounts of dissolved organic matter (DOM) into the water column during recurring blooms in coastal waters and inland seas. The released DOM includes dissolved organic carbon, nitrogen and phosphorus, in a complex mixture of both known and unknown compounds, and is a rich nutrient source for heterotrophic bacteria. The metabolic activity of heterotrophic bacteria during and after phytoplankton blooms can hence be expected to reflect the characteristics of the released DOM. With this in mind, we wanted to investigate if bacterioplankton could be used as “living sensors” of phytoplankton DOM quantity and quality, and to trace the flow of nutrients in the ecosystem. We used transcriptional activity from Baltic Sea bacterial isolates (Polaribacter sp. BAL334 (Flavobacteriia) and Brevundimonas sp. BAL450 (Alphaproteobacteria)) exposed to DOM derived from the dinoflagellate Prorocentrum minimum in exponential and stationary growth phases respectively. We observed strong responses both in terms of physiology – bacterial abundance – and the expressed metabolic pathways – e.g. Membrane Transport, Fatty Acids, Lipids and Isoprenoids – of the populations in samples exposed to dinoflagellate DOM compared with controls. Particularly striking was the increased expression of Ton and Tol transport systems, commonly associated with uptake of complex molecules, in both isolates. Equally important were the differences in metabolic responses between the two isolates, caused by differences in gene repertoire between them, emphasizing the importance of separating the responses of different taxa in analyses of community sequence data. Differences in response to DOM sourced from exponentially and stationary growing dinoflagellates were less pronounced, although not absent, than differences between the bacterial isolates. This suggests that shifts in metabolism during the different phases of a phytoplankton bloom might be detectable in individual bacterial populations. To conclude, our work opened a door to the future use of bacterioplankton as living sensors of environmental status, particularly with respect to phytoplankton blooms.

  • 231. Keller, Judith I
    et al.
    Shriver, W Gregory
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Griekspoor, Petra
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Olsen, Björn
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Prevalence of Campylobacter in wild birds of the mid-Atlantic region, USA.2011In: Journal of Wildlife Diseases, ISSN 0090-3558, E-ISSN 1943-3700, Vol. 47, no 3, p. 750-754Article in journal (Refereed)
    Abstract [en]

    We evaluated the occurrence of three Campylobacter species--C. jejuni, C. coli, and C. lari--from 333 wild bird fecal samples collected at Tri-State Bird Rescue and Research in Newark, Delaware, in 2008. Using multiplex polymerase chain reaction, we detected C. jejuni from six avian families with an overall prevalence rate of 7.2%. We did not detect any other Campylobacter species. Campylobacter jejuni prevalence ranged widely between different avian families with crows (Corvidae) and gulls (Laridae) having the highest prevalence rates (23% and 25%, respectively).

  • 232.
    Khoshkhoo, Mohammad
    et al.
    Luleå University of Technology.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Shchukarev, Andrey
    Umeå University.
    Sandström, Åke
    Luleå University of Technology.
    Electrochemical simulation of redox potential development in bioleaching of a pyritic chalcopyrite concentrate2014In: Hydrometallurgy, ISSN 0304-386X, E-ISSN 1879-1158, Vol. 144-145, p. 7-14Article in journal (Refereed)
    Abstract [en]

    The majority of the world's copper reserves are bound in the sulphide mineral chalcopyrite (CuFeS2), but supply of the copper is hindered by the recalcitrance of chalcopyrite to (bio)leaching. The main reason for the slow rate of chalcopyrite dissolution is the formation of a layer on the surface of the mineral that hinders dissolution, termed “passivation”. The nature of this layer and the role of microorganisms in chalcopyrite leaching behaviour are still under debate. Moderately thermophilic bioleaching of a pyritic chalcopyrite concentrate was mimicked in an electrochemical vessel to investigate the effect of the absence and presence of microorganisms in copper dissolution efficiency. Data from the redox potential development during bioleaching was used to program a redox potential controller in an electrochemical vessel to accurately reproduce the same leaching conditions in the absence of microorganisms. Two electrochemical experiments were carried out with slightly different methods of redox potential control. Despite massive precipitation of iron as jarosite in one of the electrochemically controlled experiments and formation of elemental sulphur in both electrochemical experiments, the efficiencies of copper dissolution were similar in the electrochemical tests as well as in the bioleaching experiment. No passivation was observed and copper recoveries exhibited a linear behaviour versus the leaching time possibly due to the galvanic effect between chalcopyrite and pyrite. The data suggest that the main role of microorganisms in bioleaching of a pyritic chalcopyrite concentrate was regeneration of ferric iron. It was also shown that the X-ray photoelectron spectroscopy measurements on the residues containing bulk precipitates cannot be employed for a successful surface characterisation.

  • 233.
    Khoshkhoo, Mohammed
    et al.
    Luleå University of Technology.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Shchukarev, Andrey
    Umeå University.
    Sandström, Åke
    Luleå University of Technology.
    Chalcopyrite leaching and bioleaching: An XPS study to characterize the nature of hindered dissolution2014In: Hydrometallurgy, ISSN 0304-386X, E-ISSN 1879-1158, Vol. 149, p. 220-227Article in journal (Refereed)
    Abstract [en]

    Chalcopyrite (CuFeS2) is both the most economically important and the most difficult copper mineral to (bio)leach. The main reason for the slow rate of chalcopyrite dissolution is the formation of a layer on the surface of the mineral that hinders dissolution, termed “passivation”. The nature of this layer is still under debate. In this work, the role of bacterial activity was examined on the leaching efficiency of chalcopyrite by mimicking the redox potential conditions during moderately thermophilic bioleaching of a pure chalcopyrite concentrate in an abiotic experiment using chemical/electrochemical methods. The results showed that the copper recoveries were equal in the presence and absence of the mixed culture. It was found that the presence of bulk jarosite and elemental sulphur in the abiotic experiment did not hamper the copper dissolution compared to the bioleaching experiment. The leaching curves had no sign of passivation, rather that they indicated a hindered dissolution. XPS measurements carried out on massive chalcopyrite samples leached in the bioleaching and abiotic experiments revealed that common phases on the surface of the samples leached for different durations of time were elemental sulphur and iron-oxyhydroxides. The elemental sulphur on the surface of the samples was rigidly bound in a way that it did not sublimate in the ultra-high vacuum environment of the XPS spectrometer at room temperature. Jarosite was observed in only one sample from the abiotic experiment but no correlation between its presence and the hindered leaching behaviour could be made. In conclusion, a multi-component surface layer consisting of mainly elemental sulphur and iron-oxyhydroxides was considered to be responsible for the hindered dissolution.

  • 234. Kim, MC
    et al.
    Kim, M-J
    Kwon, Y-K
    Lindberg, A. Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Joh, S-J
    Kwon, H-M
    Lee, Y-J
    Kwon, J-H
    Development of duck hepatitis A virus type 3 vaccine and its use to protect ducklings against infections2009In: Vaccine, ISSN 0264-410X, E-ISSN 1873-2518, Vol. 27, no 8, p. 6688-6694Article in journal (Refereed)
    Abstract [en]

    A variant type of duck hepatitis A virus (DHAV), DHAV-3 was recently discovered in South Korea and China. Sequence analyses verified that the variant is genetically or serologically different from the DHAV-1 and DHAV-2 types. Duck hepatitis had been reported in South Korea since 1985 and an attenuated DHAV-1 vaccine had efficiently prevented epidemics of DHAV-1 until 2002. Despite the DHAV-1 based vaccine in use the novel DHAV-3 circulating in South Korea remains to be a threat to duckling farming. To develop a live attenuated vaccine against DHAV-3, a representative isolate, AP-04203, was therefore attenuated by repeated passages in SPF chicken embryos 100 times. The 100th passaged virus, AP-04203P100, did not cause clinical sign and mortality in 1-day-old ducklings as well as reversion of virulence capacity. The ducklings vaccinated with AP-04203P100 virus (10(3.0) ELD(50)/0.2 ml) on 1-day-old age via the intramuscular injection were well protected from 2 days after challenge with pathogenic AP04203P1 virus via the intramuscular route. In addition, the vaccine candidate also exhibited complete protection against currently circulating pathogenic DHAV-3 isolates. In conclusion, we demonstrate that the live attenuated virus, AP-04203P100, is a promising vaccine candidate facilitating the prevention of duck hepatitis caused by DHAV-3 around East Asia including South Korea.

  • 235. Knowles, N J
    et al.
    Hovi, T
    Hyypiä, T
    King, A M Q
    Lindberg, A. Michael
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Pallansch, M A
    Palmenberg, A C
    Simmonds, P
    Skern, T
    Stanway, G
    Yamashita, T
    Zell, R
    Family - Picornaviridae2012In: Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses / [ed] Andrew M.Q. King, Elliot Lefkowitz, Michael J. Adams and Eric B. Carstens, San Diego - London: Elsevier, 2012, p. 855-881Chapter in book (Refereed)
    Abstract [en]

    This chapter focuses on Picornaviridae family whose member genuses includeEnterovirus, Cardiovirus, Aphthovirus, Hepatovirus, and Parechovirus. The virions of this family consist of a capsid with no envelope and surrounds a core of ssRNA. Hydrated native particles are 30 nm in diameter, but vary from 22 to 30 nm in electron micrographs due to drying and flattening during preparation. The virions contain one molecule of positive sense, ssRNA, and possess a single long ORF. The UTRs at both termini contain regions of secondary structure, which are essential to genome function. In addition to the major CPs, 1A, 1B, 1C and 1D, and 3B (VPg), small amounts of 1AB (VP0) are commonly seen in lieu of one or more copies of 1A and 1B. Protein 1A is small in hepatoviruses, and 1AB is uncleaved in avihepatoviruses, kobuviruses, parechoviruses, and a number of unclassified picornaviruses. Some picornaviruses carry a sphingosine-like molecule in a cavity located inside 1D, and protein 1A generally has a molecule of myristic acid covalently attached to the amino terminal glycine. The virion RNA is infectious and serves as both the genome and the viral mRNA. Infection is generally cytolytic, but persistent infections are common with some species and reported with others. Poliovirus infected cells undergo extensive vacuolation as membranes are reorganized into viral replication complexes.

  • 236.
    Kraus, Robert H. S.
    et al.
    Wageningen University, The Netherlands.
    van Hooft, Pim
    Wageningen University, The Netherlands.
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Latorre-Margalef, Neus
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Ydenberg, Ronald C.
    Wageningen University, The Netherlands ; Simon Fraser University, Canada.
    Prins, Herbert H. T.
    Wageningen University, The Netherlands.
    Avian influenza surveillance with FTA cards: field methods, biosafety, and transportation issues solved2011In: Journal of Visualized Experiments, ISSN 1940-087X, E-ISSN 1940-087X, no 54, article id 2832Article in journal (Refereed)
    Abstract [en]

    Avian Influenza Viruses (AIVs) infect many mammals, including humans(1). These AIVs are diverse in their natural hosts, harboring almost all possible viral subtypes(2). Human pandemics of flu originally stem from AIVs(3). Many fatal human cases during the H5N1 outbreaks in recent years were reported. Lately, a new AIV related strain swept through the human population, causing the 'swine flu epidemic'(4). Although human trading and transportation activity seems to be responsible for the spread of highly pathogenic strains(5), dispersal can also partly be attributed to wild birds(6, 7). However, the actual reservoir of all AIV strains is wild birds. In reaction to this and in face of severe commercial losses in the poultry industry, large surveillance programs have been implemented globally to collect information on the ecology of AIVs, and to install early warning systems to detect certain highly pathogenic strains(8-12). Traditional virological methods require viruses to be intact and cultivated before analysis. This necessitates strict cold chains with deep freezers and heavy biosafety procedures to be in place during transport. Long-term surveillance is therefore usually restricted to a few field stations close to well equipped laboratories. Remote areas cannot be sampled unless logistically cumbersome procedures are implemented. These problems have been recognised(13, 14) and the use of alternative storage and transport strategies investigated (alcohols or guanidine)(15-17). Recently, Kraus et al.(18) introduced a method to collect, store and transport AIV samples, based on a special filter paper. FTA cards(19) preserve RNA on a dry storage basis(20) and render pathogens inactive upon contact(21). This study showed that FTA cards can be used to detect AIV RNA in reverse-transcription PCR and that the resulting cDNA could be sequenced and virus genes and determined. In the study of Kraus et al.(18) a laboratory isolate of AIV was used, and samples were handled individually. In the extension presented here, faecal samples from wild birds from the duck trap at the Ottenby Bird Observatory (SE Sweden) were tested directly to illustrate the usefulness of the methods under field conditions. Catching of ducks and sample collection by cloacal swabs is demonstrated. The current protocol includes up-scaling of the work flow from single tube handling to a 96-well design. Although less sensitive than the traditional methods, the method of FTA cards provides an excellent supplement to large surveillance schemes. It allows collection and analysis of samples from anywhere in the world, without the need to maintaining a cool chain or safety regulations with respect to shipping of hazardous reagents, such as alcohol or guanidine.

  • 237.
    Kupka, Daniel
    et al.
    Slovak Academy of Sciences, Košice, Slovakia.
    Liljeqvist, Maria
    Umeå University.
    Nurmi, Pauliina
    Tampere University of Technology, Tampere, Finland.
    Puhakka, Jaakko A
    Tampere University of Technology, Tampere, Finland.
    Tuovinen, Olli H
    Tampere University of Technology, Tampere, Finland ; Ohio State University, USA.
    Dopson, Mark
    Umeå University.
    Oxidation of elemental sulfur, tetrathionate and ferrous iron by the psychrotolerant Acidithiobacillus strain SS3.2009In: Research in Microbiology, ISSN 0923-2508, E-ISSN 1769-7123, Vol. 160, no 10, p. 767-774Article in journal (Refereed)
    Abstract [en]

    Mesophilic iron and sulfur-oxidizing acidophiles are readily found in acid mine drainage sites and bioleaching operations, but relatively little is known about their activities at suboptimal temperatures and in cold environments. The purpose of this work was to characterize the oxidation of elemental sulfur (S(0)), tetrathionate (S4O6(2-)) and ferrous iron (Fe2+) by the psychrotolerant Acidithiobacillus strain SS3. The rates of elemental sulfur and tetrathionate oxidation had temperature optima of 20 degrees and 25 degrees C, respectively, determined using a temperature gradient incubator that involved narrow (1.1 degrees C) incremental increases from 5 degrees to 30 degrees C. Activation energies calculated from the Arrhenius plots were 61 and 89 kJ mol(-1) for tetrathionate and 110 kJ mol(-1) for S(0) oxidation. The oxidation of elemental sulfur produced sulfuric acid at 5 degrees C and decreased the pH to approximately 1. The low pH inhibited further oxidation of the substrate. In media with both S(0) and Fe2+, oxidation of elemental sulfur did not commence until all available ferrous iron was oxidized. These data on sequential oxidation of the two substrates are in keeping with upregulation and downregulation of several proteins previously noted in the literature. Ferric iron was reduced to Fe2+ in parallel with elemental sulfur oxidation, indicating the presence of a sulfur:ferric iron reductase system in this bacterium.

  • 238.
    Kupka, Daniel
    et al.
    Slovak Academy of Sciences, Košice, Slovakia.
    Rzhepishevska, Olena I.
    Umeå University.
    Dopson, Mark
    Umeå University.
    Lindström, E. Börje
    Umeå University.
    Karnachuk, Olia V.
    Tomsk State University, Tomsk, Russia.
    Tuovinen, Olli H.
    Ohio State University, USA.
    Bacterial oxidation of ferrous iron at low temperatures2007In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 97, no 6, p. 1470-1478Article in journal (Refereed)
    Abstract [en]

    This study comprises the first report of ferrous iron oxidation by psychrotolerant, acidophilic iron-oxidizing bacteria capable of growing at 5 degrees C. Samples of mine drainage-impacted surface soils and sediments from the Norilsk mining region (Taimyr, Siberia) and Kristineberg (Skellefte district, Sweden) were inoculated into acidic ferrous sulfate media and incubated at 5 degrees C. Iron oxidation was preceded by an approximately 3-month lag period that was reduced in subsequent cultures. Three enrichment cultures were chosen for further work and one culture designated as isolate SS3 was purified by colony isolation from a Norilsk enrichment culture for determining the kinetics of iron oxidation. The 16S rRNA based phylogeny of SS3 and two other psychrotolerant cultures, SS5 from Norilsk and SK5 from Northern Sweden, was determined. Comparative analysis of amplified 16S rRNA gene sequences showed that the psychrotolerant cultures aligned within Acidithiobacillus ferrooxidans. The rate constant of iron oxidation by growing cultures of SS3 was in the range of 0.0162-0.0104 h(-1) depending on the initial pH. The oxidation kinetics followed an exponential pattern, consistent with a first order rate expression. Parallel iron oxidation by a mesophilic reference culture of Acidithiobacillus ferrooxidans was extremely slow and linear. Precipitates harvested from the 5 degrees C culture were identified by X-ray diffraction as mixtures of schwertmannite (ideal formula Fe(8)O(8)(OH)(6)SO(4)) and jarosite (KFe(3)(SO(4))(2)(OH)(6)). Jarosite was much more dominant in precipitates produced at 30 degrees C. Biotechnol. Bioeng. 2007;97:1470-1478. (c) 2007 Wiley Periodicals, Inc.

  • 239. Landner, L.
    et al.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Oil spill protection in the Baltic based on investigations into the ecological effects of oil pollution and of chemicals used to combat oil spills1975In: Journal of Water Pollution Control Federation, ISSN 0043-1303, Vol. 47, p. 796-809Article in journal (Refereed)
  • 240.
    Lara, Elena
    et al.
    Institut de Ciències del Mar (CSIC), Spain.
    Holmfeldt, Karin
    University of Arizona, USA.
    Solonenko, Natalie
    University of Arizona, USA.
    Sà, Elisabet Laia
    Institut de Ciències del Mar (CSIC), Spain.
    Ignacio-Espinoza, J Cesar
    University of Arizona, USA.
    Cornejo-Castillo, Francisco M
    Institut de Ciències del Mar (CSIC), Spain.
    Verberkmoes, Nathan C
    Oak Ridge National Laboratory, USA.
    Vaqué, Dolors
    Institut de Ciències del Mar (CSIC), Spain.
    Sullivan, Matthew B
    University of Arizona, USA.
    Acinas, Silvia G
    Institut de Ciències del Mar (CSIC), Spain.
    Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the northwestern Mediterranean Sea.2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 1, article id e0114829Article in journal (Refereed)
    Abstract [en]

    Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new 'rare virosphere' phage-host model system.

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  • 241. Larsson, U.
    et al.
    Hagström, Åke
    The National Environmental Protection Board, Brackish Water Toxicology Laboratory, Studsvik, S-611 01 Nyköping.
    Phytoplankton extracellular release as an energy source for the growth of pelagic bacteria1979In: Marine Biology, ISSN 1230-7688, Vol. 52, p. 199-206Article in journal (Refereed)
  • 242. Larsson, U.
    et al.
    Linden, O.
    Hagström, Åke
    Department of Microbiology, University of Umeå .
    Al-Alawi, Z.S.
    Pelagic bacterial and phytoplankton in a subtropical marine environment exposed to chronic oil contamination.1990In: Oil and Chemical Pollution, ISSN 0269-8579, Vol. 7, no 2, p. 129-142Article in journal (Refereed)
    Abstract [en]

    The abundance and production of pelagic bacteria, phytoplankton primary production and chlorophyll content were studied in coastal waters receiving the effluent from an oil refinery in the Arabian Gulf. The area also receives unknown amounts of other effluents rich in organic matter and nutrients. The abundance of bacteria was measured by epifluorescent direct counts, and productivity was estimated by 3H-thymidine uptake measurements. The results showed a clear stimulation of the primary productivity as well as elevated amounts of chlorophyll a in the area receiving the effluent. Both bacterial abundances and production were an order of magnitude higher in a small area close to the refinery outlet, but dropped rapidly and reached background values outside an impacted area of c 10 km2. The increased bacterial production in this area corresponded to a substrate demand of 4 to 11 tonnes of carbon per day, 4 to 12 times the daily discharge of some 0·9 tonnes of carbon in the form of petroleum hydrocarbons from the oil refinery. These data, plus the low petroleum hydrocarbon concentrations found in the sediments and in bivalves outside the impacted area, suggest that bacterial degradation of the petroleum hydrocarbons from the refinery could be a major process restricting the area impacted by oil pollution. 

  • 243.
    Latorre-Margalef, Neus
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Georgia, USA.
    Avril, Alexis
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Tolf, Conny
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Olsen, Björn
    Uppsala University.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?2016In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 82, no 4, p. 1147-1153Article in journal (Refereed)
    Abstract [en]

    Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given Ct value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data.

  • 244.
    Latorre-Margalef, Neus
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Grosbois, Vladimir
    International Research Center in Agriculture for Development, France.
    Wahlgren, John
    Karolinska Institutet.
    Munster, Vincent J.
    Erasmus Medical Center, The Netherlands ; National Institutes of Health, USA.
    Tolf, Conny
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fouchier, Ron A. M.
    Erasmus Medical Center, The Netherlands.
    Osterhaus, Albert D. M. E.
    Erasmus Medical Center, The Netherlands.
    Olsen, Björn
    Uppsala University.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Heterosubtypic Immunity to Influenza A Virus Infections in Mallards May Explain Existence of Multiple Virus Subtypes2013In: PLoS Pathogens, ISSN 1553-7366, E-ISSN 1553-7374, Vol. 9, no 6, article id e1003443Article in journal (Refereed)
    Abstract [en]

    Wild birds, particularly duck species, are the main reservoir of influenza A virus (IAV) in nature. However, knowledge of IAV infection dynamics in the wild bird reservoir, and the development of immune responses, are essentially absent. Importantly, a detailed understanding of how subtype diversity is generated and maintained is lacking. To address this, 18,679 samples from 7728 Mallard ducks captured between 2002 and 2009 at a single stopover site in Sweden were screened for IAV infections, and the resulting 1081 virus isolates were analyzed for patterns of immunity. We found support for development of homosubtypic hemagglutinin (HA) immunity during the peak of IAV infections in the fall. Moreover, re-infections with the same HA subtype and related prevalent HA subtypes were uncommon, suggesting the development of natural homosubtypic and heterosubtypic immunity (p-value = 0.02). Heterosubtypic immunity followed phylogenetic relatedness of HA subtypes, both at the level of HA clades (p-value = 0.04) and the level of HA groups (p-value = 0.05). In contrast, infection patterns did not support specific immunity for neuraminidase (NA) subtypes. For the H1 and H3 Clades, heterosubtypic immunity showed a clear temporal pattern and we estimated within-clade immunity to last at least 30 days. The strength and duration of heterosubtypic immunity has important implications for transmission dynamics of IAV in the natural reservoir, where immune escape and disruptive selection may increase HA antigenic variation and explain IAV subtype diversity.

  • 245.
    Latorre-Margalef, Neus
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Gunnarsson, Gunnar
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Munster, V J
    Fouchier, R A M
    Osterhaus, A D M E
    Elmberg, J
    Olsen, Björn
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Wallensten, Anders
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Fransson, T
    Brudin, Lars
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Waldenström, Jonas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Does Influenza A affect body condition of wild mallard ducks, or vice versa? A reply to Flint & Franson2009In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 276, no 1666, p. 2347-2349Article in journal (Refereed)
  • 246.
    Latorre-Margalef, Neus
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Gunnarsson, Gunnar
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Munster, V.J.
    Fouchier, R.A.M.
    Osterhaus, A.D.M.E.
    Elmberg, Johan
    Olsen, Björn
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Wallensten, Anders
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Haemig, Paul D.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Fransson, Thord
    Brudin, Lars
    University of Kalmar, School of Pure and Applied Natural Sciences. Kalmar County Hospital.
    Waldenström, Jonas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Effects of influenza A virus infection on migrating mallard ducks2009In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 276, no 1659, p. 1029-1036Article in journal (Refereed)
    Abstract [en]

    The natural reservoir of influenza A virus is waterfowl, particularly dabbling ducks (genus Anas). Although it has long been assumed that waterfowl are asymptomatic carriers of the virus, a recent study found that low-pathogenic avian influenza (LPAI) infection in Bewick's swans (Cygnus columbianus bewickii) negatively affected stopover time, body mass and feeding behaviour. In the present study, we investigated whether LPAI infection incurred ecological or physiological costs to migratory mallards (Anas platyrhynchos) in terms of body mass loss and staging time, and whether such costs could influence the likelihood for long-distance dispersal of the avian influenza virus by individual ducks. During the autumn migrations of 2002-2007, we collected faecal samples (n = 10 918) and biometric data from mallards captured and banded at Ottenby, a major staging site in a flyway connecting breeding and wintering areas of European waterfowl. Body mass was significantly lower in infected ducks than in uninfected ducks (mean difference almost 20 g over all groups), and the amount of virus shed by infected juveniles was negatively correlated with body mass. There was no general effect of infection on staging time, except for juveniles in September, in which birds that shed fewer viruses stayed shorter than birds that shed more viruses. LPAI infection did not affect speed or distance of subsequent migration. The data from recaptured individuals showed that the maximum duration of infection was on average 8.3 days (s.e. 0.5), with a mean minimum duration of virus shedding of only 3.1 days (s.e. 0.1). Shedding time decreased during the season, suggesting that mallards acquire transient immunity for LPAI infection. In conclusion, deteriorated body mass following infection was detected, but it remains to be seen whether this has more long-term fitness effects. The short virus shedding time suggests that individual mallards are less likely to spread the virus at continental or intercontinental scales.

  • 247.
    Latorre-Margalef, Neus
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Georgia, Dept Populat Hlth, Coll Vet Med, Southeastern Cooperat Wildlife Dis Study, Athens, GA 30602 USA.
    Tolf, Conny
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Grosbois, Vladimir
    Int Res Ctr Agr Dev CIRAD UPR AGIRs, Anim & Integrate Risk Management, F-34398 Montpellier, France.
    Avril, Alexis
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bengtsson, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wille, Michelle
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Osterhaus, Albert D M E
    Erasmus MC, Dept Virol, Rotterdam, Netherlands.
    Fouchier, Ron A M
    Erasmus MC, Dept Virol, Rotterdam, Netherlands.
    Olsen, Björn
    Uppsala Univ.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Long-term variation in influenza A virus prevalence and subtype diversity in migratory mallards in northern Europe.2014In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, no 1781, p. Article ID: UNSP 20140098-Article in journal (Refereed)
    Abstract [en]

    Data on long-term circulation of pathogens in wildlife populations are seldom collected, and hence understanding of spatial-temporal variation in prevalence and genotypes is limited. Here, we analysed a long-term surveillance series on influenza A virus (IAV) in mallards collected at an important migratory stopover site from 2002 to 2010, and characterized seasonal dynamics in virus prevalence and subtype diversity. Prevalence dynamics were influenced by year, but retained a common pattern for all years whereby prevalence was low in spring and summer, but increased in early autumn with a first peak in August, and a second more pronounced peak during October-November. A total of 74 haemagglutinin (HA)/neuraminidase (NA) combinations were isolated, including all NA and most HA (H1-H12) subtypes. The most common subtype combinations were H4N6, H1N1, H2N3, H5N2, H6N2 and H11N9, and showed a clear linkage between specific HA and NA subtypes. Furthermore, there was a temporal structuring of subtypes within seasons based on HA phylogenetic relatedness. Dissimilar HA subtypes tended to have different temporal occurrence within seasons, where the subtypes that dominated in early autumn were rare in late autumn, and vice versa. This suggests that build-up of herd immunity affected IAV dynamics in this system.

  • 248.
    Leblond, Jeffrey D.
    et al.
    Middle Tennessee State University, USA.
    Dahmen, Aaron S.
    Middle Tennessee State University, USA.
    Lebret, Karen
    Lund University.
    Rengefors, Karin
    Lund University.
    Sterols of the Green-Pigmented, Freshwater Raphidophyte, Gonyostomum semen, from Scandinavian Lakes2013In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 60, no 4, p. 399-405Article in journal (Refereed)
    Abstract [en]

    Sterols are a class of membrane-reinforcing, ringed lipids which have a long history of examination in algae as a means of deriving chemotaxonomic relationships and as potential lipidic biomarkers. The Raphidophyceae represent a class of harmful, bloom-forming, marine and freshwater algae. To date, there have been four published examinations of their sterol composition, focusing primarily on brown-pigmented, marine species within the genera, Chattonella, Fibrocapsa, and Heterosigma. Lacking in these examinations has been the species Gonyostomum semen Ehrenb., which is a green-pigmented, freshwater raphidophyte with a worldwide distribution. The goal of this study was to examine the sterol composition of this nuisance alga, determine the potential of using its sterol profile as a biomarker, and finally to determine if there is any intraspecific variability between isolates. We have examined 21 isolates of G. semen from a number of Scandinavian lakes, and all were found to produce two major sterols, 24-ethylcholesta-5,22E-dien-3-ol and 24-ethylcholest-5-en-3-ol, and 24-methylcholest-5-en-3-ol as a minor sterol; the presence of 24-ethylcholesta-5,22E-dien-3-ol differentiates G. semen from brown-pigmented, marine raphidophytes which generally lack it. The results of this study indicate that isolates of G. semen from geographically separate lakes across Finland and Scandinavia have the same sterol biosynthetic pathway, and that there is no evolutionary divergence between the isolates with regard to sterol composition. The sterols of G. semen are not considered to be useful biomarkers for this particular organism because they are commonly found in other algae and plants.

  • 249.
    Lewis, Nicola S.
    et al.
    Univ Cambridge, UK.
    Verhagen, Josanne H.
    Erasmus MC, Netherlands.
    Javakhishvili, Zurab
    Ilia State Univ, Rep of Georgia.
    Russell, Colin A.
    Univ Cambridge, UK.
    Lexmond, Pascal
    Erasmus MC, Netherlands.
    Westgeest, Kim B.
    Erasmus MC, Netherlands.
    Bestebroer, Theo M.
    Erasmus MC, Netherlands.
    Halpin, Rebecca A.
    J Craig Venter Inst, USA.
    Lin, Xudong
    J Craig Venter Inst, USA.
    Ransier, Amy
    J Craig Venter Inst, USA.
    Fedorova, Nadia B.
    J Craig Venter Inst, USA.
    Stockwel, Timothy B.
    J Craig Venter Inst, USA.
    Latorre-Margalef, Neus
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Georgia, USA.
    Olsen, Björn
    Uppsala Univ.
    Smith, Gavin
    Duke NUS Grad Med Sch, Singapore.
    Bahl, Justin
    Duke NUS Grad Med Sch, Singapore ; Univ Texas Houston, USA..
    Wentworth, David E.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fouchier, Ron A. M.
    Erasmus MC, Netherlands.
    de Graaf, Miranda
    Erasmus MC, Netherlands.
    Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data2015In: Journal of General Virology, ISSN 0022-1317, E-ISSN 1465-2099, Vol. 96, p. 2050-2060Article in journal (Refereed)
    Abstract [en]

    Low pathogenic avian influenza A viruses (IAVs) have a natural host reservoir in wild waterbirds and the potential to spread to other host species. Here, we investigated the evolutionary, spatial and temporal dynamics of avian IAVs in Eurasian wild birds. We used whole-genome sequences collected as part of an intensive long-term Eurasian wild bird surveillance study, and combined this genetic data with temporal and spatial information to explore the virus evolutionary dynamics. Frequent reassortment and co-circulating lineages were observed for all eight genomic RNA segments over time. There was no apparent species-specific effect on the diversity of the avian IAVs. There was a spatial and temporal relationship between the Eurasian sequences and significant viral migration of avian lAVs from West Eurasia towards Central Eurasia. The observed viral migration patterns differed between segments. Furthermore, we discuss the challenges faced when analysing these surveillance and sequence data, and the caveats to be borne in mind when drawing conclusions from the apparent results of such analyses.

  • 250.
    Liljeqvist, Maria
    et al.
    Umea Univ, Sweden.
    Ossandon, Francisco J.
    Univ Andres Bello, Chile.
    Gonzalez, Carolina
    Univ Andres Bello, Chile ; Fraunhofer Chile Res Fdn, Chile.
    Rajan, Sukithar
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Stell, Adam
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Valdes, Jorge
    Fraunhofer Chile Res Fdn, Chile.
    Holmes, David S.
    Univ Andres Bello, Chile.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Umeå Univ, Sweden.
    Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream2015In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 91, no 4, article id fiv011Article in journal (Refereed)
    Abstract [en]

    An acid mine drainage (pH 2.5-2.7) stream biofilm situated 250 m below ground in the low-temperature (6-10 degrees C) Kristineberg mine, northern Sweden, contained a microbial community equipped for growth at low temperature and acidic pH. Metagenomic sequencing of the biofilm and planktonic fractions identified the most abundant microorganism to be similar to the psychrotolerant acidophile, Acidithiobacillus ferrivorans. In addition, metagenome contigs were most similar to other Acidithiobacillus species, an Acidobacteria-like species, and a Gallionellaceae-like species. Analyses of the metagenomes indicated functional characteristics previously characterized as related to growth at low temperature including cold-shock proteins, several pathways for the production of compatible solutes and an anti-freeze protein. In addition, genes were predicted to encode functions related to pH homeostasis and metal resistance related to growth in the acidic metal-containing mine water. Metagenome analyses identified microorganisms capable of nitrogen fixation and exhibiting a primarily autotrophic lifestyle driven by the oxidation of the ferrous iron and inorganic sulfur compounds contained in the sulfidic mine waters. The study identified a low diversity of abundant microorganisms adapted to a low-temperature acidic environment as well as identifying some of the strategies the microorganisms employ to grow in this extreme environment.

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